Conformational RNA epitopes were discovered because autoantibodies in the sera of patients with systemic autoimmune diseases are directly reactive with discrete structural elements in U1 snRNA, transfer RNA and ribosomal RNA. See Wilusz, J. & Keene, J. D. (1986) J. Biol. Chem. 261, 5467-5472; Deutscher, S. L. & Keene, J. D. (1988) Proc. Natl. Acad. Sci. USA 85, 3299-3303; Uchiumi, T. et al. (1991) J. Biol. Chem. 266, 2054-2062. These and other studies indicated that autoantibodies recognize and bind with high specificity to unique and restricted regions of cellular RNA molecules in a manner much like their binding to epitopes on proteins.
Immune reactivity with specific regions of RNA molecules was unexpected since nucleic acids are poorly immunogenic and the net negative charge on the surfaces of antibodies disfavor interactions with negatively charged phosphate backbones of RNA and DNA. Historically, the reactivity of RNA with antibodies has been viewed with skepticism as an epiphenomenon resulting from accidental crossreactivity of RNAs (now termed aptamers) with other cellular immunogens or to result from an unexplainable presentation of RNA fragments to the immune system following a breakdown in discrimination of self from nonself. However, it has been shown that unique RNA molecules can be selected in vitro from combinatorial RNA libraries to bind to antibody binding sites, indicating that conformational RNA epitopes may result from crossreactivity between RNAs and proteins that is discrete, specific, and non-coincidental. See, e.g., Tsai, D. S., et al. (1992) Proc. Natl. Acad. Sci. USA 89, 8864-8868; Tsai, D. S. & Keene, J. D. (1993) J. Immunol. 150, 1137-1145; Kenan, D. J., et al. (1994) TIBS 19, 57-64; Doudna, J. A., et al. (1995) Proc. Natl. Acad. Sci. USA 92, 2355-2359.
J. Keene et al., PCT Application No. PCT/US93/08210, describes methods of making epitopes and nucleic acids embodying the epitopes so made. Specifically, a method is described wherein an antibody can be employed to derive a nonproteinaceous mimetic ligand that binds to the same site on the antibody to which the original antigen bound. The method involves combining an antigen binding protein (e.g., an antibody, a T cell receptor) which binds the immunogen with a degenerate pool of nucleic acid species, and then recovering a nucleic acid species bound by said binding protein from the degenerate pool.
It would be highly desirable to have a means for making a nucleic acid that is immunologically cross-reactive with other molecules without the need to resort to a degenerate pool of nucleic acids.
It would also be highly desirable to have a means for making a non-nucleic acid molecule that is immunologically cross-reactive with a nucleic acid, when an antigen binding protein that specifically binds that nucleic acid is known.